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February 2020, Volume 70, Issue 2

Research Article

Comparison of phenotypic methods with mecA gene based polymerase chain reaction for Methicillin-resistant Staphylococcus aureus detection

Aneela Khawaja  ( Post Graduate Medical Institute, Lahore )
Faiqa Arshad  ( Post Graduate Medical Institute, Lahore, Pakistan. )
Idrees Khan  ( Virologist Center of Excellence and Molecular Biology (CEMB), Punjab University, Pakistan. )


Objective: To determine methicillin resistance in staphylococcus aureus by different phenotypic methods, and to evaluate their accuracy with mecA gene polymerase chain reaction for methicillin-resistant staphylococcus aureus detection.

Methods: The descriptive cross-sectional study was conducted from January to December 2015 at the Post- Graduate Medical Institute, Lahore, Pakistan, and comprised consecutive, non-repetitive clinical isolates of methicillin-resistant staphylococcus aureus that were screened with oxacillin disk 1μg and cefoxitin disk 30μg by Kirby-Bauer method using Clinical and Laboratory Standards Institute guideline. The isolates were cultured on oxacillin screen and mannitol salt agar, and subjected to latex agglutination for penicillin-binding protein 2aand polymerase chain reaction for mecA gene. Data was analysed using SPSS 20.

Results: All the 105 isolates were resistant on oxacillin and cefoxitin disk diffusion test, but 95(90.47%) were positive for mecA gene by latex agglutination and polymerase chain reaction. The sensitivity of oxacillin salt agar, mannitol salt agar and latex agglutination was 94.31%, 96.73% and 98.95%, respectively. Keeping polymerase chain reaction as the gold standard, the specificity and diagnostic accuracy of latex agglutination were 77.77% and 97.14% respectively, which was the highest among all the phenotypic methods.

Conclusion: Latex agglutination method can be proposed as a swiftly reliable diagnostic technique for the detection of mecA gene in methicillin-resistant staphylococcus aureus isolates in resource-constrained settings where molecular methods are limited.

Keywords: Methicillin resistant staphylococcus aureus, Oxacillin, Cefoxitin, Latex agglutination, PCR. (JPMA 70: 276; 2020)




Methicillin resistance is an outcome of modification in the assembly of bacterial cell wall by the penicillin binding protein 2a(PBP2a) conferred by the mecA gene.1 This additional mecA gene is found in methicillin-resistant staphylococci, with no allelic equivalence in methicillinsusceptible staphylococci.2 The phenotypic expression of resistance can be variable even with genetic uniformity being affected by cultural conditions, temperature and osmolality of the medium. Phenotypic resistance to -lactam antibiotic is demonstrated in terms of decreased zone of inhibition for oxacillin and cefoxitin or increased minimal inhibitory concentration (MIC). The heterogeneous resistance pattern may cause difficulties in detecting methicillinresistant staphylococcus (S.) aureus (MRSA) by phenotypic methods.3 The current study was planned to compare the precision of different conventional phenotypic methods in detecting MRSA and to evaluate their sensitivity and specificity with polymerase chain reaction (PCR) as the gold standard for mecA gene.


Material and Methods


The descriptive cross-sectional study was conducted at the Pathology Department of the Post-Graduate Medical Institute (PGMI), Lahore, Pakistan, from January to December 2015, and comprised clinical specimens from patients admitted in different clinical wards of the Lahore General Hospital (LGH). All the samples were processed according to the standard operating guidelines in the PGMI microbiology laboratory. All the specimens were inoculated on blood agar and MacConkey agar, prepared as per the instructions of the manufacturer. The plates were incubated at 35-37°C aerobically. Following standard microbiological techniques, preliminary identification of S. aureus isolates was done by observing the colony morphology on blood agar plates, finding -positive cocci in clusters on gram staining and positive catalase test. Further, biochemical tests, like coagulase and deoxyribonucleic acid-ase (DNAase), were performed for the confirmation of S. aureus. For all the phenotypic and genotypic test runs, MRSAATCC 33591 and methicillin-susceptible S. aureus (MSSA)ATCC 25923 were used as positive and negative controls respectively.4 Initial screening was performed by disk diffusion test following the 2016 guidelines recommended by the Clinical and Laboratory Standards Institute (CLSI).4 A bacterial suspension of each strain (0.5 McFarland standards) was inoculated on Mueller Hinton agar (MHA). Oxacillin disk 1 g was applied and plates were incubated at 35°C for 24 hrs. An inhibition zone of <10mm was considered oxacillin (methicillin) resistance.5 The phenotypic resistance to methicillin was ascertained by modified Kirby-Bauer using 30μg cefoxitin disc (Oxoid) on MHA, according to the CLSI guiding principles.4 For each strain, a bacterial suspension, adjusted according to 0.5 McFarland turbidity standards, was prepared and inoculated on MHA. The plates were incubated at 35°C and zone of inhibition was determined after 24 hours. The results were interpreted according to CLSI criteria, i.e. zone of <21mm was considered resistant and >22mm was considered sensitive.5 MHA containing 4% sodium chloride (NaCl) and 6 g/ml oxacillin was prepared. Each isolate was inoculated in one quadrant (10 l of 0.5 McFarland standards) and incubated at 35°C for 24 hours. The plates were inspected carefully in transmitted light for any growth. Any growth after 24 hours indicated oxacillin resistance.6 Mannitol salt agar (MSA) containing cefoxitin (8μg/ml) was prepared according to instructions given by the manufacturer. All the isolates were inoculated on the prepared plates along with positive and negative controls. The plates were incubated at 35°C and first checked after 24 hours. Yellow coloured colonies produced due to mannitol fermentation indicated methicillin resistance. The results were recorded at 48 hours.7,8 All the S. aureus isolates showing resistance by disk diffusion method were tested for mecA gene product PBP2a using latex agglutination (LA) kit (Oxoid, DR0900). The procedure was carried out according to the manufacturer's instructions using colonies on MHA. Latex particles activated with monoclonal antibodies directed against PBP2a particularly bind with methicillin-resistant staphylococci to produce clumping noticeable to the naked eye. MSSA does not agglutinate the latex particles. All the reagents were stored at 2-8°C. Each strain was tested simultaneously with a negative control latex suspension.9 All the MRSA isolates were grown in nutrient broth by incubating in a shaking incubator at 37°C for 24 hours. Boiling method was used for DNA extraction. The supernatant was collected and stored at -20°C for PCR reaction. PCR was carried out to confirm the existence of mecA gene in MRSA. The mecA gene was detected using primers for mecA gene (Table-1).

DNA amplification was performed as follows: An initial denaturation step of 5min at 94°C; followed by 35 cycles of denaturation step at 95°C for 45s, annealing step at 58°C for 45s, and extension step at 72°C for 45s; and a final extension at 72°C for 5min. The PCR amplification products (310 bp) were analysed by electrophoresis on 1.2% agarose gel stained with ethidium bromide (10mg/ml), using DNA ladder (1kb) and visualised under ultraviolet (UV) light.10 Data was analysed using SPSS 20. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic accuracy (DA) of all the phenotypic methods was calculated using mecA gene PCR as the gold standard.




All the 105(100%) isolates were (resistant to oxacillin and cefoxitin by disk diffusion method. Among these isolates, 92(87.61%), 95(90.47%), and 97(92.38%) isolates produced positive results for oxacillin screen agar (OSA), MSA (Figure-1)

and LA (Figure-2),

respectively. The PCR amplification for the mecA gene detected 95(90.47%) mecA-positive and 10(9.52%) mecA-negative isolates. Out of the 95 mecA PCR-positive isolates, 83(87.4%), 89(93.6%) and 95(100%) strains were correctly identified as MRSA by OSA, MSA and LA, respectively. The sensitivity of OSA, MSA and LA was 94.31, 96.73 and 98.95%, respectively. Among the 10 mecA negative isolates; 4(40%), 3(30%) and 2(20%) isolates were incorrectly identified by OSA, MSA and LA, respectively. LA gave the lowest false negative result compared to MSA and OSA, while LA had the highest sensitivity (Table-2).




MRSA is one of the most challenging bacterial pathogens that presently affect patients in hospitals as well as in the community.11 Worldwide, dramatic increase in MRSA burden has started to pose a great difficulty in the selection of antibiotics in the management and treatment of infections caused by this super bug.12 Here comes the importance of rapid and accurate detection of MRSA in clinical microbiology laboratories not only for choosing the appropriate antibiotic therapy for the individual patient, but also to avoid treatment failure as well as to control the spread of MRSA.13 A wide range of phenotypic methods have been developed to detect MRSA, but they vary in sensitivity and specificity.14 Moreover, these tests may not ensure appropriate and timely treatment of all the patients suffering from MRSA infections.15 Detection of the mecA gene by PCR is the gold standard, but not always available in routine laboratories and is not affordable.16 LA test to identify mecA gene product PBP2a is a sensitive, rapid and accurate method for the routine use in resourceconstrained laboratories.9 The current study evaluated the diagnostic ability of different phenotypic methods in detecting MRSA. These methods were OSA, MSA and LA tests. Sensitivity of these phenotypic methods was evaluated. Comparison was done against the PCR assay results. Data showed that the OSA test gave the lowest performance values in comparison to the other phenotypic methods. MRSA detection by OSA had sensitivity of 94.31%. The sensitivity of OSA was the lowest among all phenotypic methods. Similar results have been shown by other studies.17,18Another study14 showed high sensitivity and specificity of OSA, mentioning that incubating the plate up to full 48 hours increases the sensitivity but the delay in getting results reduces the efficacy of this method. The current study found MSA sensitivity of 96.73% more suitable than OSA's 94.31%, but it was less than LA which showed 98.95%. Other studies have shown good sensitivity and specificity of MSA as well.19,20 However, the present results are not in concordance with a study7 in which MSA showed lower sensitivity 89.13% than OSA, suggesting that several strains of MRSA might fail to grow on MSA due to its high salt concentration. By analysing the performance of different phenotypic tests, the current study found that best overall performance of LA was comparable with PCR. LA test was found to be more sensitive and specific (98.95% and 77.77% respectively) for the detection of MRSA. Moreover, PPV, NPV and DA of LA were the highest among all the tests i.e., 97.93%, 87.50% and 97.14% respectively. Several studies have shown comparable results with LA sensitivity being >97%.6,15,21-23 A study proved that the combination of cefoxitin disk diffusion with LA improves sensitivity and specificity to detect MRSA isolates.24 However, two strains that were tested positive in the LA test showed negative results for mecA by PCR in the current study. Similar discrepancy was reported with one strain earlier as well.25 The present study found that out of 105 cefoxitin resistant MRSA strains, 95 were mecA gene-positive on PCR and 10 were mecA-negative. The results are in concordance with the study in India that detected 92 isolates mecA-positive and 10 isolates as mecA-negative out of 102 cefoxitin resistant MRSA stains.7 Other studies have shown even higher mecA-negative isolates.26,27 A novel mecA homologue called mecC have been reported in different parts of the world.28,29These isolates are resistant to oxacillin or cefoxitin, but show negative results for mecA on PCR.26




OSA and MSA tests were less sensitive and specific than LA test. The results of LA test more in line with PCR. For the early and precise identification of MRSA, cefoxitin disc diffusion method must be used with another reliable method, preferably LA test, in routine clinical microbiology laboratories in resource-limited settings as an alternative to PCR. This will help enhance and facilitate MRSA detection.


Disclaimer: None.

Conflict of Interest: None.

Source of Funding: None.




1. Peacock SJ, Paterson GK. Mechanisms of methicillin resistance in Staphylococcus aureus. Annu Rev biochem. 2015; 84:577-601.

2. Rahbar M, Yaghoobi M, Fattahi A. Comparison of different laboratory methods for detection of methicillin resistant Staphylococcus aureus. Pak J Med Sci. 2006; 22:442-5.

3. Brown DF, Edwards DI, Hawkey PM, Morrison D, Ridgway GL, Towner KJ, et al. Guidelines for the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). J Antimicrob Chemother. 2005; 56:1000-18.

4. Clinical and Laboratory Standards Institute (CLSI). M100-S26. Performance standards for antimicrobial susceptibility testing: 26th informational supplement. Wayne, PA: Clinical and Laboratory Standards Institute; 2016.

5. Rostami S, Moosavian M, Shoja S, Torabipour M, Farshadzadeh Z. Comparison of mecA gene-based PCR with CLSI cefoxitin and oxacillin disc diffusion methods for detecting methicillin resistance in Staphylococcus aureus clinical isolates. Afr J Microbiol Res. 2013; 7:2438-41.

6. Alipour F, Ahmadi M, Javadi S. Evaluation of different methods to detect methicillin resistance in Staphylococcus aureus (MRSA). J Infect Public Health. 2014; 7:186-91.

7. Kali A, Stephen S, Umadevi S. Laboratory evaluation of phenotypic detection methods of methicillin-resistant Staphylococcus aureus. Biomed J. 2014; 37:411-4.

8. Ahmed MO. Cefoxitin mannitol salt agar for selective isolation of methicilin resistant Staphylococcus aureus. Ibnosina J Med Biomed Sci. 2014; 6:31-3.

9. Ali SM, Bayoumi EA, Alshazly TA. Molecular Identification of Methicillin Resistant Staphylococcus aureus and Evaluation of Panton-Valentine Leukocidin Gene as a Sole Marker for CA-MRSA. J Am Sci. 2013; 9:108-15.

10. Zhang K, McClure JA, Elsayed S, Conly JM. Novel staphylococcal cassette chromosome mec type, tentatively designated type VIII, harboring class Amec and type 4 ccr gene complexes in a

Canadian epidemic strain of methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother. 2009; 53:531-40.

11. Patil NR, Ghorpade MV. Comparison of conventional phenotypic methods for detection of methicillin resistant Staphylococcus aureus. Int J Res Dev Pharm Life Sci. 2016; 5:2039-44.

12. Pramodhini S, Thenmozhivalli PR, Selvi R, Dillirani V, Vasumathi A, Agatha D. Comparison of various phenotypic methods and mecA based PCR for the detection of MRSA. J Clin Diagnostic Res. 2011; 5:1359-62.

13. Farahani A, Mohajeri P, Gholamine B, Rezaei M, Abbasi H. Comparison of different phenotypic and genotypic methods for the detection of methicillin-resistant Staphylococcus aureus. N Am J Med Sci. 2013; 5:637-40.

14. Panda RK, Mahapatra A, Mallick B, Chayani N. Evaluation of genotypic and phenotypic methods for detection of methicillin resistant Staphylococcus aureus in a tertiary care hospital of Eastern Odisha. J Med Microbiol. 2011; 60:1613-6.

15. Datta P, Gulati N, Singla N, Vasdeva HR, Bala K, Chander J, et al. Evaluation of various methods for the detection of meticillinresistant Staphylococcus aureus strains and susceptibility patterns. J Med Microbiol. 2011; 60:1613-6.

16. Ghanwate N, Thakare P, Bhise PR, Gawande S. Colorimetric method for rapid detection of Oxacillin resistance in Staphylococcus aureus and its comparison with PCR for mecA gene. Sci Rep. 2016; 6:23013.

17. Mathews AA, Thomas M, Appalaraju B, Jayalakshmi J. Evaluation and comparison of tests to detect methicillin resistant S. aureus. Indian J Pathol Microbiol. 2010; 53:79-82.

18. Buchan BW, Ledeboer NA. Identification of two borderline oxacillin-resistant strains of Staphylococcus aureus from routine nares swab specimens by one of three chromogenic agars evaluated for the detection of MRSA. Am J Clin Pathol. 2010; 134:921-7.

19. Yamazumi T, Marshall SA, Wilke WW, Diekema DJ, Pfaller MA, Jones RN. Comparison of the Vitek Gram-Positive Susceptibility 106 card and the MRSA-screen latex agglutination test for determining oxacillin resistance in clinical bloodstream isolates of Staphylococcus aureus. J Clin Microbiol. 2001; 39:53-6.

20. Stoakes L, Reyes R, Daniel J, Lennox G, John MA, Lannigan R, et al. Prospective comparison of a new chromogenic medium, MRSASelect, to CHROMagar MRSA and mannitol-salt medium supplemented with oxacillin or cefoxitin for detection of methicillin-resistant Staphylococcus aureus. J Clin Microbiol. 2006; 44:637-9.

21. Louie L, Matsumura SO, Choi E, Louie M, Simor AE. Evaluation of three rapid methods for detection of methicillin resistance in Staphylococcus aureus. Eur J Clin Microbiol Infect Dis. 2001; 20:267-70.

22. Rohrer S, Tschierske M, Zbinden R, Berger-Bachi B. Improved methods for detection of methicillin-resistant Staphylococcus aureus. Eur J Clin Microbiol Infect Dis. 2001; 20:267-70.

23. Iraz M, Tekerekoglu MS, Otlu B, Ay S. Comparison of an automated system with four phenotypic methods for the detection of methicillin-resistant Staphylococcus aureus. Afr J Microb Res. 2012; 6:764-9.

24. Bandaru NR, Budati S. Evaluation of four phenotypic methods for the rapid identification of methicillin resistant Staphylococcus aureus. Inter J Res Med Sci. 2017; 4:2271-5.

25. Sakoulas G, Gold HS, Venkataraman L, DeGirolami PC, Eliopoulos GM, Qian Q. Methicillin-resistant Staphylococcus aureus: comparison of susceptibility testing methods and analysis of mecA-positive susceptible strains. J Clin Microbiol. 2001; 39:3946- 51.

26. Broekema NM, Van TT, Monson TA, Marshall SA, Warshauer DM. Comparison of cefoxitin and oxacillin disk diffusion methods for detection of mecA-mediated resistance in Staphylococcus aureus in a large-scale study. J Clin Microbiol. 2009; 47:217-9.

27. Anand KB, Agrawal P, Kumar S, Kapila K. Comparison of cefoxitin disc diffusion test, oxacillin screen agar, and PCR for mecA gene for detection of MRSA. Indian J Med Microbiol. 2009; 27:27-9.

28. Garcia-Alvarez L, Holden MT, Lindsay H, Webb CR, Brown DF, Curran MD, et al. Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis. 2011; 11:595-603.

29. Romero-Gomez MP, Mora-Rillo M, Lazaro-Perona F, Gomez-Gil MR, Mingorance J. Bacteraemia due to meticillin-resistant Staphylococcus aureus carrying the mecC gene in a patient with urothelial carcinoma. J Med Microbiol. 2013; 62:1914-6.

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